Development of a Non-Invasive Plasma-Based Test to Stratify Non-Small Cell Lung Cancer Patients for Targeted Therapies Lung cancer is the most common and lethal cancer worldwide, accounting for 1.8 million new cases and 1.6 million deaths in 2012 (www.lung.org). In the United States alone, there will be approximately 221,200 new cases and 158,000 deaths in 2015. Non-Small Cell Lung Cancer (NSCLC) accounts for 85% of lung cancer (DeSantis et al., 2014). More than 50% of NSCLC patients are diagnosed with metastatic disease and receive systemic treatment. Targeted therapies developed recently have increased median survival by 50% in metastatic NSCLC patients whose tumors harbor genetic alterations in specific, clinically actionable, cancer driver genes (Kris et al., 2014). Therefore, clinical guidelines for metastatic NSCLC recommend molecular testing of these genes in stage IV patients to inform choice of targeted therapy (Lindeman, Cagle, Beasley, Chitale, Dacic, Giaccone, Jenkins, Kwiatkowski, Saldivar, Squire, Thunnissen, & Ladanyi, 2013), however, rely on the availability of adequate tumor tissue, which excludes approximately 35% of metastatic NSCLC patients from targeted interventions (Travis et al., 2013). The purpose of this phase I proposal is to develop and validate LungSelect, a non-invasive, plasma-based molecular test for the identification of genetic alterations (both sequence mutations and structural alterations) in clinically actionable cancer driver genes from circulating cell-free DNA (cfDNA) of metastatic NSCLC patients. [We envision that the LungSelect test will enable approximately 30,000 metastatic NSCLC patients to be stratified for FDA-approved targeted therapies and late stage clinical trials annually, while overcoming the need for tumor tissue that is mandatory for existing tissue-based molecular tests.] Circulating cell-free DNA fragments (cfDNA) are shed into the bloodstream by cells in the body. A fraction of cfDNA in the plasma of cancer patients is shed from tumor cells and carries genetic alterations specific to tumor cells (Crowley, Di Nicolantonio, Loupakis, & Bardelli, 2013). Reliable detection of tumor specific alterations in plasma can help stratify patients for targeted therapies and overcome the need for tumor tissue by traditional molecular tests. To achieve this, Personal Genome Diagnostics (PGDx) proposes to develop and validate LungSelect, a non-invasive, plasma-based molecular test for the identification of genetic alterations in clinically actionable genes in cfDNA of NSCLC patients. The current phase I proposal consists of three specific aims: (1) development of the LungSelect test using digital next-generation sequencing based approaches, (2) analytical validation of LungSelect, and (3) preliminary evaluation of concordance between the genetic alterations identified in matched tumor and plasma samples using LungSelect. Pending success of the phase I proposal, we will apply for phase II funding to further validate the assay and establish its clinical validity by demonstrating the concordance between time-matched tissue and plasma samples in a large cohort of cancer patients. Additionally, we plan to commercialize the assay to afford NSCLC patients without tumor tissue, who currently receive conventional chemotherapy alone, the clinical benefit of existing FDA-approved targeted therapies.